Contacts of the strand formed by residues 86 - 97 (chain A) in PDB entry 5FL6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 5.7 2.0 + - - -
45A LEU* 4.2 13.1 - - - +
81A ALA* 3.3 3.8 - - - -
82A LEU* 3.0 65.5 + - + +
83A GLY* 2.9 22.2 + - - +
84A PRO 4.0 7.2 - - - +
85A GLY* 1.3 79.1 - - - +
87A GLU* 1.3 59.3 + - - +
88A TYR* 3.4 17.7 + - + +
194A GLN* 3.2 28.5 + - - +
209A ILE* 4.1 11.1 - - - +
196B GLU* 5.3 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 5.6 2.2 - - - +
80A MET 3.7 3.8 - - - +
81A ALA* 4.5 12.4 - - + +
85A GLY* 3.7 12.2 + - - +
86A ARG* 1.3 80.0 - - - +
88A TYR* 1.3 69.5 + - - +
124A SER* 3.7 4.7 + - - -
125A THR* 3.2 41.3 + - + +
27B ARG* 3.0 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.5 6.8 - - - +
80A MET* 2.8 50.3 + - + +
82A LEU* 3.8 20.7 - - + +
86A ARG* 3.4 28.3 + - + +
87A GLU* 1.3 87.0 - - - +
89A ARG* 1.3 64.4 + - - +
122A HIS* 3.7 16.8 - - + -
123A LEU 3.3 8.3 - - - -
124A SER* 3.3 30.2 - - - -
125A THR* 4.2 4.4 - - - +
138A GLY* 2.7 37.0 + - - -
140A LEU 4.1 0.2 - - - -
141A ALA* 3.6 27.8 - - + -
209A ILE* 4.3 4.2 - - - +
137B PRO* 5.3 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 5.7 6.3 - - - +
78A LEU 3.2 13.2 - - - +
79A GLU* 4.7 14.5 - - + +
88A TYR* 1.3 78.6 - - - +
90A ALA* 1.3 65.5 + - - +
91A LEU* 3.6 4.8 + - + +
122A HIS* 3.2 3.7 - - - -
123A LEU* 2.9 38.1 + - + +
125A THR* 3.6 42.5 + - + +
127A PHE 5.2 4.2 + - - -
75D PRO* 5.6 1.4 - - - +
76D PRO* 3.4 44.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.1 5.8 - - + -
74A LEU* 3.8 21.8 - - + +
75A PRO 4.1 15.4 - - - +
76A PRO* 5.7 0.5 - - - +
78A LEU* 2.9 32.0 + - + +
89A ARG* 1.3 75.5 - - - +
91A LEU* 1.3 64.1 + - - +
120A VAL* 4.5 0.7 - - + -
121A VAL 3.8 2.5 - - - +
122A HIS* 3.4 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 4.0 5.0 - - - +
74A LEU* 2.9 28.5 + - - +
89A ARG* 4.1 9.4 - - + +
90A ALA* 1.3 80.6 - - - +
92A GLN* 1.3 73.9 + - + +
121A VAL* 2.9 21.5 + - + +
122A HIS 4.5 3.8 - - - -
123A LEU* 3.8 33.2 - - + +
130A VAL* 3.2 33.7 - - + -
140A LEU* 4.9 1.6 - - + -
268A Y0R 5.4 2.7 - - - +
128D ALA* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.4 30.4 + - + +
72A LEU 3.3 14.8 - - - +
73A THR* 4.4 3.4 - - + +
74A LEU* 3.8 9.6 - - - +
91A LEU* 1.3 87.4 - - + +
93A LEU* 1.3 63.8 + - - +
94A HIS* 2.8 23.0 + - - -
120A VAL* 3.6 2.6 - - - +
121A VAL* 2.9 45.1 + - + +
268A Y0R 3.4 29.2 + - - +
1261A GOL 3.4 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 6.3 0.2 - - + -
70A VAL 5.8 0.2 - - - +
71A GLN* 3.3 4.3 - - - +
72A LEU* 2.8 61.3 + - + +
74A LEU* 4.1 6.3 - - + +
92A GLN* 1.3 77.9 - - - +
94A HIS* 1.3 66.6 + - - +
95A LEU* 5.2 4.5 - - + -
118A ILE* 4.0 20.6 - - + -
119A HIS 3.1 14.8 - - - +
120A VAL* 4.0 14.4 - - + -
160A LEU* 4.4 9.2 - - + -
181A ILE* 3.7 22.7 - - + -
184A LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 3.4 9.4 - - - +
70A VAL 3.2 17.3 - - - +
71A GLN* 4.0 2.7 - - - -
92A GLN* 2.8 22.0 + - - +
93A LEU* 1.3 77.7 - - - +
95A LEU* 1.3 68.3 + - - +
96A HIS* 3.3 10.5 - + - -
118A ILE* 3.5 4.0 - - - +
119A HIS* 2.9 39.2 + - + +
121A VAL* 3.7 7.9 - - + -
268A Y0R 3.1 20.0 + - - -
1260A ZN 2.1 33.7 - - - -
1261A GOL 3.5 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 2.5 24.7 + - - -
70A VAL* 3.4 14.4 + - + +
93A LEU* 5.2 4.5 - - + -
94A HIS* 1.3 81.2 - - - +
96A HIS* 1.3 68.4 + - - +
97A TRP* 3.4 16.6 - - + -
117A GLU 3.3 5.2 - - - +
118A ILE* 3.6 39.9 - - + -
147A LEU* 4.4 4.7 - - + -
157A TYR* 4.3 21.3 - - + -
160A LEU* 5.7 8.5 - - + -
161A LEU* 4.9 8.1 - - + -
227A LEU* 3.7 31.9 - - + -
242A ASN* 3.4 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.7 14.8 - - - -
69A SER* 5.3 2.7 - - - -
94A HIS* 3.3 8.5 - + - -
95A LEU* 1.3 80.2 + - - +
97A TRP* 1.3 61.6 + - - +
104A GLY 3.6 12.2 - - - +
106A GLU* 3.4 26.9 + - + -
116A ALA* 3.2 6.4 - - - +
117A GLU* 2.8 39.0 + - + +
119A HIS* 3.2 21.2 + + - -
200A THR* 4.2 0.9 - - - -
201A THR* 5.1 1.8 - - + -
242A ASN* 2.7 29.8 + - - +
268A Y0R 3.9 3.4 - - - -
1260A ZN 2.1 37.1 - - - -
1261A GOL 5.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 4.0 3.1 - - - -
70A VAL* 3.8 15.9 - - + -
95A LEU* 3.4 35.0 - - + -
96A HIS* 1.3 75.6 - - - +
98A GLY* 1.3 83.0 + - - +
104A GLY* 3.5 13.5 + - - +
115A PRO 3.9 5.8 - - - +
116A ALA* 4.0 5.4 - - + -
227A LEU* 3.6 52.8 + - + -
228A SER* 3.5 17.3 - - - +
231A LEU* 3.7 24.2 - - + -
239A LEU* 2.9 41.7 + - + -
240A GLN* 3.7 3.0 - - - +
241A LEU* 3.2 14.9 + - - -
242A ASN* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il